Hear about the latest tech updates for Oxford Nanopore Technologies as well as talks from local scientists about their latest work using nanopore technology.
There will also be an opportunity to submit questions throughout the talks, which will be answered in the live Q&A sessions following each presentation.
The agenda below is subject to change.
10:15 - 10:20 am | Welcome & introduction | Manuela Saathoff & François Berdou Oxford Nanopore Technologies Ltd |
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10:20 - 10:40 am | Genomics and metatranscriptomic applications of nanopore sequencing technology to microbial and viral clinical diagnostics | Alban Ramette University of Bern |
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10:40 - 11:00 am | A splice-isoform analysis of endogenous NMD targets in human cells using Nanopore sequencing | Evangelos Karousis University of Bern |
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11:00 - 11:35 am | An update from Oxford Nanopore Technologies | Barbara Ottolini Oxford Nanopore Technologies Ltd |
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11:35 - 11:55 am | Methylome Analysis: A Success Story in Digital Pathology Diagnostics | Jürgen Hench University Hospital Basel |
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11:55 - 12:30 pm | Analysis of nanopore sequence data; from research tools to EPI2ME Labs | Stephen Rudd Oxford Nanopore Technologies Ltd |
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12:30 - 12:35 pm | Closing remarks | Manuela Saathoff & François Berdou Oxford Nanopore Technologies Ltd |
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Alban Ramette, Institute for Infectious Diseases, University of Bern
With a background in microbial ecology, statistics and molecular biology, Dr. Alban Ramette is principal investigator of the Bioinformatics and Biostatistics group at the Institute for Infectious Diseases (IFIK) in Bern, Switzerland. His research focuses on classical and genomic epidemiology of viral and bacterial pathogens, and on the implementation of next generation sequencing technologies for clinical applications. His laboratory was the first worldwide to receive the ISO 17025 accreditation for clinical applications of nanopore-based sequencing in January 2019 and the first Swiss nanopore sequencing service provider in October 2018.
Abstract
Genomics and metatranscriptomic applications of nanopore sequencing technology to microbial and viral clinical diagnostics
In this presentation, Dr Ramette will present our genomic and metatranscriptomic analyses of human enteroviruses directly from clinical material, and our latest genomic sequencing of SARS-Cov-2 isolates obtained from clinical samples. Altogether the presentation provides insights on successful implementation of nanopore sequencing to pathogen identification and characterization in the clinical laboratory.
Evangelos Karousis, Dept of Chemistry and Biochemistry, University of Bern
Evangelos is a postdoc in Oliver Mühlemann’s group at the Department of Chemistry and Biochemistry, University of Bern, Switzerland. He is interested in post-transcriptional mRNA regulation in mammalian cells and applies Nanopore sequencing to identify endogenous mRNAs that are sensitive to nonsense-mediated mRNA decay. He is a biochemist from Greece with a background in transcriptomics, RNA decay, and in vitro translation.
Abstract
A splice-isoform analysis of endogenous NMD targets in human cells using Nanopore sequencing
Nonsense-mediated mRNA decay (NMD) is a translation-dependent RNA degradation pathway that targets mRNAs with premature termination codons as well as endogenous mRNAs that encode full-length proteins. For an isoform-specific analysis of endogenous NMD targets, we applied cDNA Nanopore sequencing in human cells under control and KD conditions of NMD factors. Our approach can detect full-length isoforms that increase in levels or even only appear when NMD is inactivated. We will present a workflow that allowed the characterization of splicing events that give rise to NMD-sensitive isoforms and the assessment of features that are present in NMD-sensitive mRNAs.
Angela Steinauer, MSCA Postdoctoral Fellow in the Hilvert Group at ETH Zurich
Dr. Angela Steinauer is an MSCA Postdoctoral Fellow in the Hilvert Group at ETH Zurich. Her research focuses on developing virus-like capsids for mRNA delivery using design and directed evolution.
Abstract
Characterizing the RNA Packaging Specificity of Evolved Virus-like Nucleocapsids Using Oxford Nanopore Sequencing
Viruses are sophisticated protein shells that selectively package their own genomes. We asked: Can we engineer a non-viral protein cage with no affinity for nucleic acids to encapsidate its own genome? Using design and directed evolution, the Aquifex aeolicus lumazine synthase capsid was evolved over four generations to package its own capsid-encoding mRNA with increasing specificity. We used ONT sequencing to characterize which RNAs are present in each generation and found that, for the first, the majority of the encapsidated RNA originates from the host, whereas for the final generation, the majority is the capsid’s own RNA genome.
Jürgen Hench, Institute for Medical Genetics and Pathology, Division of Neuropathology, University Hospital Basel
Dr. Jürgen Hench is a board-certified neuropathologist and also responsible for molecular pathology diagnostics at the University Hospital Basel. He has a strong interest in implementing artificial intelligence strategies in neuropathological diagnostics, most importantly in tumor classification.
Abstract
Methylome Analysis: A Success Story in Digital Pathology Diagnostics
Brain tumor methylation classification and genomic copy number analysis has started to become the de facto standard in neuro-oncological diagnostics in 2018. However, the reference method, microarray analysis, is expensive and often requires turnaround times of weeks. As an alternative, nanopore sequencing of tumor DNA extracts provides precise genome-wide methylation and copy number information. Nanopore WGS data are compared with established reference microarray-based datasets to obtain tumor classification. In contrast to arrays, this process currently takes a few hours, enabling same-day molecular brain tumor classification through a pipeline that can also be implemented in low-income regions.
François Berdou, Strategic Relationship Manager, Oxford Nanopore Technologies
Manuela Saasthoff, Strategic Account Manager, Oxford Nanopore Technologies